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Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant.
Bedotto, Marielle; Fournier, Pierre-Edouard; Houhamdi, Linda; Levasseur, Anthony; Delerce, Jeremy; Pinault, Lucile; Padane, Abdou; Chamieh, Amanda; Tissot-Dupont, Hervé; Brouqui, Philippe; Sokhna, Cheikh; Azar, Eid; Saile, Rachid; Mboup, Souleymane; Bitam, Idir; Colson, Philippe; Raoult, Didier.
  • Bedotto M; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Fournier PE; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marsei
  • Houhamdi L; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Levasseur A; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marsei
  • Delerce J; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Pinault L; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Padane A; Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Arrondissement 4 rue 2D1, pôle urbain de Diamniadio, Dakar, Senegal.
  • Chamieh A; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France; Saint George Hospital University Medical Center, University of Balaman
  • Tissot-Dupont H; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
  • Brouqui P; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marsei
  • Sokhna C; Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Campus International IRD-UCAD de l'IRD, Dakar, Senegal; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Vecteurs - Infections Tropicales et Méditerranéennes (V
  • Azar E; Saint George Hospital University Medical Center, University of Balamand, Beirut, Lebanon.
  • Saile R; Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University of Casablanca, Morocco.
  • Mboup S; Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Arrondissement 4 rue 2D1, pôle urbain de Diamniadio, Dakar, Senegal.
  • Bitam I; Ecole supérieure en Sciences de l'aliment et des Industries Agro-Alimentaires, Alger, Algeria.
  • Colson P; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marsei
  • Raoult D; IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marsei
J Clin Virol ; 139: 104814, 2021 06.
Article in English | MEDLINE | ID: covidwho-1174353
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT

INTRODUCTION:

The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. MATERIALS AND

METHODS:

We aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant.

RESULTS:

All 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93 %) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 2018/3960 (51%) patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6 %) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR.

DISCUSSION:

Our in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in about half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: J Clin Virol Journal subject: Virology Year: 2021 Document Type: Article Affiliation country: J.jcv.2021.104814

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: J Clin Virol Journal subject: Virology Year: 2021 Document Type: Article Affiliation country: J.jcv.2021.104814